null Mon 24 Dec 00:10:00 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fna-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fna-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fna-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-3.6-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-3.6-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:10:05 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-3.6-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 525 and 0 Target number of residues in the AU: 525 Target solvent content: 0.6593 Checking the provided sequence file Detected sequence length: 357 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 714 Adjusted target solvent content: 0.54 Input MTZ file: 2fna-3.6-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 4 Cell parameters: 55.380 108.390 70.600 90.000 100.307 90.000 Input sequence file: 2fna-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5712 target number of atoms Had to go as low as 0.80 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 69.461 3.600 Wilson plot Bfac: 84.33 9441 reflections ( 98.49 % complete ) and 0 restraints for refining 6318 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3289 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2897 (Rfree = 0.000) for 6318 atoms. Found 40 (40 requested) and removed 41 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 6477 seeds are put forward NCS extension: 0 residues added, 6477 seeds are put forward Round 1: 314 peptides, 59 chains. Longest chain 13 peptides. Score 0.340 Round 2: 372 peptides, 59 chains. Longest chain 14 peptides. Score 0.452 Round 3: 387 peptides, 57 chains. Longest chain 18 peptides. Score 0.494 Round 4: 390 peptides, 50 chains. Longest chain 19 peptides. Score 0.551 Round 5: 390 peptides, 53 chains. Longest chain 17 peptides. Score 0.529 Taking the results from Round 4 Chains 51, Residues 340, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 11554 restraints for refining 5176 atoms. 10143 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2330 (Rfree = 0.000) for 5176 atoms. Found 19 (33 requested) and removed 29 (16 requested) atoms. Cycle 2: After refmac, R = 0.2184 (Rfree = 0.000) for 5113 atoms. Found 18 (33 requested) and removed 17 (16 requested) atoms. Cycle 3: After refmac, R = 0.2118 (Rfree = 0.000) for 5108 atoms. Found 4 (32 requested) and removed 20 (16 requested) atoms. Cycle 4: After refmac, R = 0.2097 (Rfree = 0.000) for 5089 atoms. Found 6 (32 requested) and removed 16 (16 requested) atoms. Cycle 5: After refmac, R = 0.2068 (Rfree = 0.000) for 5077 atoms. Found 5 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.34 Search for helices and strands: 0 residues in 0 chains, 5241 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 5264 seeds are put forward Round 1: 328 peptides, 60 chains. Longest chain 12 peptides. Score 0.360 Round 2: 375 peptides, 53 chains. Longest chain 16 peptides. Score 0.504 Round 3: 396 peptides, 58 chains. Longest chain 18 peptides. Score 0.502 Round 4: 384 peptides, 54 chains. Longest chain 18 peptides. Score 0.511 Round 5: 384 peptides, 54 chains. Longest chain 19 peptides. Score 0.511 Taking the results from Round 5 Chains 54, Residues 330, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 11878 restraints for refining 5177 atoms. 10612 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2189 (Rfree = 0.000) for 5177 atoms. Found 21 (33 requested) and removed 24 (16 requested) atoms. Cycle 7: After refmac, R = 0.2077 (Rfree = 0.000) for 5150 atoms. Found 6 (33 requested) and removed 18 (16 requested) atoms. Cycle 8: After refmac, R = 0.2031 (Rfree = 0.000) for 5134 atoms. Found 2 (32 requested) and removed 17 (16 requested) atoms. Cycle 9: After refmac, R = 0.2076 (Rfree = 0.000) for 5118 atoms. Found 2 (32 requested) and removed 16 (16 requested) atoms. Cycle 10: After refmac, R = 0.1986 (Rfree = 0.000) for 5099 atoms. Found 2 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 5294 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 5308 seeds are put forward Round 1: 357 peptides, 62 chains. Longest chain 17 peptides. Score 0.400 Round 2: 393 peptides, 59 chains. Longest chain 18 peptides. Score 0.489 Round 3: 382 peptides, 60 chains. Longest chain 15 peptides. Score 0.462 Round 4: 403 peptides, 57 chains. Longest chain 18 peptides. Score 0.521 Round 5: 395 peptides, 57 chains. Longest chain 17 peptides. Score 0.508 Taking the results from Round 4 Chains 57, Residues 346, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 11908 restraints for refining 5175 atoms. 10581 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2121 (Rfree = 0.000) for 5175 atoms. Found 19 (33 requested) and removed 22 (16 requested) atoms. Cycle 12: After refmac, R = 0.1995 (Rfree = 0.000) for 5162 atoms. Found 6 (33 requested) and removed 17 (16 requested) atoms. Cycle 13: After refmac, R = 0.1944 (Rfree = 0.000) for 5145 atoms. Found 2 (33 requested) and removed 16 (16 requested) atoms. Cycle 14: After refmac, R = 0.1918 (Rfree = 0.000) for 5129 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 15: After refmac, R = 0.1902 (Rfree = 0.000) for 5111 atoms. Found 2 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 5279 seeds are put forward NCS extension: 10 residues added (6 deleted due to clashes), 5289 seeds are put forward Round 1: 343 peptides, 63 chains. Longest chain 11 peptides. Score 0.364 Round 2: 374 peptides, 56 chains. Longest chain 17 peptides. Score 0.479 Round 3: 376 peptides, 56 chains. Longest chain 22 peptides. Score 0.483 Round 4: 368 peptides, 53 chains. Longest chain 17 peptides. Score 0.492 Round 5: 371 peptides, 56 chains. Longest chain 16 peptides. Score 0.474 Taking the results from Round 4 Chains 55, Residues 315, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 11723 restraints for refining 5178 atoms. 10430 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2271 (Rfree = 0.000) for 5178 atoms. Found 22 (33 requested) and removed 18 (16 requested) atoms. Cycle 17: After refmac, R = 0.2173 (Rfree = 0.000) for 5167 atoms. Found 10 (33 requested) and removed 17 (16 requested) atoms. Cycle 18: After refmac, R = 0.2088 (Rfree = 0.000) for 5157 atoms. Found 6 (33 requested) and removed 16 (16 requested) atoms. Cycle 19: After refmac, R = 0.2049 (Rfree = 0.000) for 5146 atoms. Found 4 (33 requested) and removed 16 (16 requested) atoms. Cycle 20: After refmac, R = 0.1990 (Rfree = 0.000) for 5131 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 5300 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5317 seeds are put forward Round 1: 337 peptides, 66 chains. Longest chain 11 peptides. Score 0.327 Round 2: 365 peptides, 59 chains. Longest chain 13 peptides. Score 0.439 Round 3: 376 peptides, 56 chains. Longest chain 19 peptides. Score 0.483 Round 4: 375 peptides, 58 chains. Longest chain 14 peptides. Score 0.465 Round 5: 375 peptides, 53 chains. Longest chain 21 peptides. Score 0.504 Taking the results from Round 5 Chains 55, Residues 322, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 11702 restraints for refining 5177 atoms. 10402 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2184 (Rfree = 0.000) for 5177 atoms. Found 19 (33 requested) and removed 21 (16 requested) atoms. Cycle 22: After refmac, R = 0.2011 (Rfree = 0.000) for 5158 atoms. Found 8 (33 requested) and removed 17 (16 requested) atoms. Cycle 23: After refmac, R = 0.1926 (Rfree = 0.000) for 5144 atoms. Found 3 (33 requested) and removed 18 (16 requested) atoms. Cycle 24: After refmac, R = 0.1898 (Rfree = 0.000) for 5124 atoms. Found 2 (32 requested) and removed 16 (16 requested) atoms. Cycle 25: After refmac, R = 0.1864 (Rfree = 0.000) for 5108 atoms. Found 2 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 5263 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 5286 seeds are put forward Round 1: 310 peptides, 57 chains. Longest chain 15 peptides. Score 0.350 Round 2: 349 peptides, 55 chains. Longest chain 16 peptides. Score 0.442 Round 3: 368 peptides, 58 chains. Longest chain 15 peptides. Score 0.453 Round 4: 368 peptides, 57 chains. Longest chain 16 peptides. Score 0.461 Round 5: 359 peptides, 56 chains. Longest chain 17 peptides. Score 0.452 Taking the results from Round 4 Chains 57, Residues 311, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 11972 restraints for refining 5178 atoms. 10785 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2089 (Rfree = 0.000) for 5178 atoms. Found 19 (33 requested) and removed 17 (16 requested) atoms. Cycle 27: After refmac, R = 0.1972 (Rfree = 0.000) for 5161 atoms. Found 9 (33 requested) and removed 16 (16 requested) atoms. Cycle 28: After refmac, R = 0.1885 (Rfree = 0.000) for 5149 atoms. Found 1 (33 requested) and removed 16 (16 requested) atoms. Cycle 29: After refmac, R = 0.1861 (Rfree = 0.000) for 5131 atoms. Found 1 (32 requested) and removed 16 (16 requested) atoms. Cycle 30: After refmac, R = 0.1833 (Rfree = 0.000) for 5116 atoms. Found 4 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 5279 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 5300 seeds are put forward Round 1: 315 peptides, 63 chains. Longest chain 11 peptides. Score 0.307 Round 2: 350 peptides, 56 chains. Longest chain 14 peptides. Score 0.436 Round 3: 374 peptides, 58 chains. Longest chain 16 peptides. Score 0.464 Round 4: 366 peptides, 51 chains. Longest chain 25 peptides. Score 0.504 Round 5: 371 peptides, 57 chains. Longest chain 26 peptides. Score 0.466 Taking the results from Round 4 Chains 51, Residues 315, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 11979 restraints for refining 5178 atoms. 10770 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2073 (Rfree = 0.000) for 5178 atoms. Found 22 (33 requested) and removed 21 (16 requested) atoms. Cycle 32: After refmac, R = 0.1878 (Rfree = 0.000) for 5161 atoms. Found 4 (33 requested) and removed 18 (16 requested) atoms. Cycle 33: After refmac, R = 0.1832 (Rfree = 0.000) for 5138 atoms. Found 3 (33 requested) and removed 18 (16 requested) atoms. Cycle 34: After refmac, R = 0.1831 (Rfree = 0.000) for 5120 atoms. Found 5 (32 requested) and removed 16 (16 requested) atoms. Cycle 35: After refmac, R = 0.1814 (Rfree = 0.000) for 5105 atoms. Found 4 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 5258 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 5282 seeds are put forward Round 1: 282 peptides, 56 chains. Longest chain 9 peptides. Score 0.300 Round 2: 333 peptides, 51 chains. Longest chain 18 peptides. Score 0.445 Round 3: 330 peptides, 51 chains. Longest chain 19 peptides. Score 0.440 Round 4: 342 peptides, 54 chains. Longest chain 15 peptides. Score 0.437 Round 5: 342 peptides, 52 chains. Longest chain 18 peptides. Score 0.454 Taking the results from Round 5 Chains 53, Residues 290, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 11967 restraints for refining 5177 atoms. 10789 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2044 (Rfree = 0.000) for 5177 atoms. Found 22 (33 requested) and removed 22 (16 requested) atoms. Cycle 37: After refmac, R = 0.1923 (Rfree = 0.000) for 5160 atoms. Found 9 (33 requested) and removed 18 (16 requested) atoms. Cycle 38: After refmac, R = 0.1904 (Rfree = 0.000) for 5145 atoms. Found 5 (33 requested) and removed 17 (16 requested) atoms. Cycle 39: After refmac, R = 0.1887 (Rfree = 0.000) for 5125 atoms. Found 6 (32 requested) and removed 16 (16 requested) atoms. Cycle 40: After refmac, R = 0.1890 (Rfree = 0.000) for 5108 atoms. Found 7 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 5262 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 5284 seeds are put forward Round 1: 277 peptides, 56 chains. Longest chain 12 peptides. Score 0.289 Round 2: 302 peptides, 50 chains. Longest chain 13 peptides. Score 0.394 Round 3: 299 peptides, 49 chains. Longest chain 13 peptides. Score 0.397 Round 4: 305 peptides, 49 chains. Longest chain 13 peptides. Score 0.409 Round 5: 280 peptides, 49 chains. Longest chain 13 peptides. Score 0.359 Taking the results from Round 4 Chains 49, Residues 256, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 12405 restraints for refining 5178 atoms. 11430 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1939 (Rfree = 0.000) for 5178 atoms. Found 15 (33 requested) and removed 17 (16 requested) atoms. Cycle 42: After refmac, R = 0.1815 (Rfree = 0.000) for 5166 atoms. Found 7 (33 requested) and removed 17 (16 requested) atoms. Cycle 43: After refmac, R = 0.1832 (Rfree = 0.000) for 5153 atoms. Found 6 (33 requested) and removed 17 (16 requested) atoms. Cycle 44: After refmac, R = 0.1873 (Rfree = 0.000) for 5141 atoms. Found 10 (32 requested) and removed 16 (16 requested) atoms. Cycle 45: After refmac, R = 0.1838 (Rfree = 0.000) for 5132 atoms. Found 14 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 5323 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5338 seeds are put forward Round 1: 253 peptides, 52 chains. Longest chain 14 peptides. Score 0.273 Round 2: 263 peptides, 47 chains. Longest chain 15 peptides. Score 0.341 Round 3: 256 peptides, 44 chains. Longest chain 16 peptides. Score 0.354 Round 4: 264 peptides, 44 chains. Longest chain 19 peptides. Score 0.371 Round 5: 273 peptides, 47 chains. Longest chain 18 peptides. Score 0.362 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 44, Residues 220, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2fna-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9441 reflections ( 98.49 % complete ) and 12599 restraints for refining 5178 atoms. 11763 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1864 (Rfree = 0.000) for 5178 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1811 (Rfree = 0.000) for 5156 atoms. Found 0 (33 requested) and removed 14 (16 requested) atoms. Cycle 48: After refmac, R = 0.1869 (Rfree = 0.000) for 5140 atoms. Found 0 (32 requested) and removed 11 (16 requested) atoms. Cycle 49: After refmac, R = 0.1880 (Rfree = 0.000) for 5127 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:10:22 GMT 2018 Job finished. TimeTaking 60.36 Used memory is bytes: 16351288